from your library on the Mendeley site: select the checkboxes beside the papers in your library, then choose 'OpenTree' from pulldown 'Add selected documents to...' list.

Tagging papers if data available

We can only include a published phylogeny in the draft tree of life if the data (tree and alignment files) is available. We are using a couple of tags to track data availability. Feel free to use other tags, but please document how you are using them.

Basic summary

Of 21 papers 4 had tree files.

From 21 papers only 7 had complete data matrices. Two of these 7 data sets still require manipulation because the data set was submitted in pdf format (not it NEXUS format) . Also only 4 of these 7 papers with data matrices were associated with the available tree files (Dryad/TreeBase).

total time estimate per paper for all tasks ~ 15 minutes (by an expert in the field)

note that this time estimate does not take into account the fact that we still need to contact the authors of – 15 – 17 papers for data sets and/or trees.

Some problems noted

Some recent papers stated that the data set could be obtained from a link, but this was not really active or working (one was from 2011!).

Sometimes authors said that paper was associated with Supporting data, but nothing was found as a Supplement.

Sometimes a data file was ultimately submitted to TreeBase or Dryad, but this was not noted in the paper itself.

Some papers (3 studies) have multiple trees in a file but it is not always clear which tree to use. The presence of multiple trees was observed to be for several reasons—different methods of analysis (MP, ML, BI), different data sets (e.g., no third positions), or multiple shortest trees.

The same problem as above is true when multiple matrices are available (3 studies)